Table 1.
Promoter motif optimization based on generating the motif that has the most occurrences in the promoter region relative to the total number of occurrences in the PBCV-1 genome. *Shown is the total number of times the motif occurred in the promoter regions. Note the same motif can occur multiple times within the same promoter region. For example, there are 91 unique genes that contain the promoter sequence ARNTTAANA; 84 of these genes contain the sequence one time and 7 genes contain the sequence twice.
| ARNTTAANA | |||
|---|---|---|---|
| Sequence | # Promoter Region | Total # in genome | # Promoter Region/ # Genome |
| ANNAANYYAANA | 78 | 208 | 0.38 |
| ANNRRNYYAANA | 99 | 344 | 0.29 |
| NNRRNTTAANA | 108 | 305 | 0.35 |
| ARNTTAANA | 98 | 222 | 0.44 |
| RNTTAANA | 165 | 563 | 0.29 |
| NTTAANA | 323 | 1278 | 0.25 |
| AATGACA | |||
| Sequence | # Promoter Region | Total # in genome | # Promoter Region/ # Genome |
| AAATGACRHH | 89 | 182 | 0.49 |
| ATGACRHH | 107 | 240 | 0.45 |
| AATGACRH | 112 | 251 | 0.45 |
| AATGACR | 116 | 269 | 0.43 |
| AATGACG | 12 | 78 | 0.15 |
| AATGACA | 104 | 191 | 0.54 |
| AATGAC | 128 | 337 | 0.38 |
| ATGACA | 127 | 403 | 0.32 |
| GTNGATAYR | |||
| Sequence | # Promoter Region | Total # in genome | # Promoter Region/ # Genome |
| NGTNGATANN | 69 | 329 | 0.21 |
| GTNGATAYR | 51 | 182 | 0.28 |
| TYGATAYR | 59 | 262 | 0.23 |
| TNGATAYR | 82 | 418 | 0.20 |
| YGATAYR | 103 | 604 | 0.17 |
| YGTYGATAY | 42 | 154 | 0.27 |
| YGTNGATAY | 48 | 194 | 0.25 |
| YGTYGATA | 45 | 189 | 0.24 |
| YGTNGAT | 84 | 513 | 0.16 |
| TNGATAY | 111 | 706 | 0.16 |